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- PDB-2iz9: MS2-RNA HAIRPIN (4ONE -5) COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2iz9
TitleMS2-RNA HAIRPIN (4ONE -5) COMPLEX
Components
  • 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*U ONEP *AP*CP*CP*CP*AP*UP*GP*U)-3'
  • MS2 COAT PROTEIN
KeywordsVIRUS/RNA / HAIRPIN / CAPSID / LEVIVIRUS / VIRUS / COMPLEX (CAPSID PROTEIN-RNA HAIRPIN) / VIRUS-RNA complex
Function / homology
Function and homology information


negative regulation of viral translation / T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
MS2 Viral Coat Protein / MS2 Viral Coat Protein / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Capsid protein
Similarity search - Component
Biological speciesENTEROBACTERIO PHAGE MS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsGrahn, E. / Stonehouse, N.J. / Adams, C.J. / Fridborg, K. / Beigelman, L. / Matulic-Adamic, J. / Warriner, S.L. / Stockley, P.G. / Liljas, L.
CitationJournal: Nucleic Acids Res. / Year: 2000
Title: Deletion of a Single Hydrogen Bonding Atom from the MS2 RNA Operator Leads to Dramatic Rearrangements at the RNA-Coat Protein Interface
Authors: Grahn, E. / Stonehouse, N.J. / Adams, C.J. / Fridborg, K. / Beigelman, L. / Matulic-Adamic, J. / Warriner, S.L. / Stockley, P.G. / Liljas, L.
History
DepositionJul 25, 2006Deposition site: PDBE / Processing site: PDBE
SupersessionJul 27, 2006ID: 1DZS
Revision 1.0Jul 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MS2 COAT PROTEIN
B: MS2 COAT PROTEIN
C: MS2 COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*U ONEP *AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*U ONEP *AP*CP*CP*CP*AP*UP*GP*U)-3'


Theoretical massNumber of molelcules
Total (without water)53,3075
Polymers53,3075
Non-polymers00
Water2,810156
1
A: MS2 COAT PROTEIN
B: MS2 COAT PROTEIN
C: MS2 COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*U ONEP *AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*U ONEP *AP*CP*CP*CP*AP*UP*GP*U)-3'
x 60


Theoretical massNumber of molelcules
Total (without water)3,198,404300
Polymers3,198,404300
Non-polymers00
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: MS2 COAT PROTEIN
B: MS2 COAT PROTEIN
C: MS2 COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*U ONEP *AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*U ONEP *AP*CP*CP*CP*AP*UP*GP*U)-3'
x 5


  • icosahedral pentamer
  • 267 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)266,53425
Polymers266,53425
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: MS2 COAT PROTEIN
B: MS2 COAT PROTEIN
C: MS2 COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*U ONEP *AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*U ONEP *AP*CP*CP*CP*AP*UP*GP*U)-3'
x 6


  • icosahedral 23 hexamer
  • 320 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)319,84030
Polymers319,84030
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: MS2 COAT PROTEIN
B: MS2 COAT PROTEIN
C: MS2 COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*U ONEP *AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*U ONEP *AP*CP*CP*CP*AP*UP*GP*U)-3'
x 10


  • crystal asymmetric unit, crystal frame
  • 533 kDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)533,06750
Polymers533,06750
Non-polymers00
Water72140
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)288.000, 288.000, 653.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, 0.866025), (-0.645497, 0.372678, 0.666667), (0.57735, -0.333333, 0.745356)
3generate(-0.309017, 0.755761, 0.57735), (-0.178411, -0.64235, 0.745356), (0.934172, 0.127322, 0.333333)
4generate(-0.309017, -0.178411, 0.934172), (0.755761, -0.64235, 0.127322), (0.57735, 0.745356, 0.333333)
5generate(0.5, -0.645497, 0.57735), (0.866025, 0.372678, -0.333333), (0.666667, 0.745356)
6generate(0.309017, 0.755761, 0.57735), (0.755761, -0.563661, 0.333333), (0.57735, 0.333333, -0.745356)
7generate(0.356822, 0.934172), (0.934172, 0.333333, -0.127322), (-0.356822, 0.872678, -0.333333)
8generate(0.309017, -0.178411, 0.934172), (0.178411, 0.975684, 0.127322), (-0.934172, 0.127322, 0.333333)
9generate(0.809017, -0.110264, 0.57735), (-0.467086, 0.475684, 0.745356), (-0.356822, -0.872678, 0.333333)
10generate(0.809017, 0.467086, 0.356822), (-0.110264, -0.475684, 0.872678), (0.57735, -0.745356, -0.333333)

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Components

#1: Protein MS2 COAT PROTEIN


Mass: 13738.464 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIO PHAGE MS2 (virus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03612
#2: RNA chain 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*U ONEP *AP*CP*CP*CP*AP*UP*GP*U)-3'


Mass: 6045.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: COAT PROTEIN-BINDING HAIRPIN / Source: (synth.) ENTEROBACTERIO PHAGE MS2 (virus)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFORMS THE PHAGE SHELL AND BINDS TO THE PHAGE RNA

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

Crystal growpH: 7.4 / Details: pH 7.40

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.927
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 9, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.927 Å / Relative weight: 1
ReflectionResolution: 2.85→40 Å / Num. obs: 161000 / % possible obs: 67 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 59.8 Å2 / Rmerge(I) obs: 0.13
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.36 / % possible all: 34

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MS2 RECOMBINANT CAPSIDS

Resolution: 2.85→40 Å / Rfactor Rfree error: 0.017 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.22 175 0.1 %RANDOM
Rwork0.2 ---
obs0.2 160971 66.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.5886 Å2 / ksol: 0.298896 e/Å3
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.32 Å
Luzzati d res low-6 Å
Luzzati sigma a0.17 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 630 0 156 3681
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.85→2.9 Å / Rfactor Rfree error: 0.122 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 6 0.2 %
Rwork0.324 3840 -
obs--32.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-4ODNA-RNA-4O
X-RAY DIFFRACTION3WATER_REP.WATER.TOP

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